Anaplasma phagocytophilum est une alpha-protéobactérie, parasite intracellulaire stricte, à localisation intra-granulocytaire et principalement vectorisée par des tiques du genre Ixodes. Elle est notamment l'agent de l'anaplasmose granulocytaire bovine, ou Tick-borne fever, une maladie provoquant d'importantes pertes économiques chez les bovins en Europe. Cette bactérie, peut également infecter un large spectre d'hôtes, tels que des ruminants sauvages ou des rongeurs. Cependant, l'épidémiologie de l'infection par A. phagocytophilum est encore mal connue. Le(s) réservoir(s) des souches de ruminants domestiques en Europe n'est/ne sont notamment pas identifié(s) à l'heure actuelle. Il est donc nécessaire d'approfondir nos connaissances dans ce domaine, notamment afin de lutter plus efficacement contre l'atteinte des bovins. L'objectif de cette thèse était de caractériser la diversité génétique des variants d'A. phagocytophilum circulant chez les ruminants en France. Pour cela, nous avons, dans un premier temps, étudié la circulation des souches d'A. phagocytophilum au sein des ruminants sauvages et domestiques en développant et en utilisant une technique MLVA (Multiple-Locus Variable-number tandem repeat Analysis). Cela nous a permis de suspecter fortement l'existence d'au moins deux cycles épidémiologiques impliquant des variants d'A. phagocytophilum présents chez les ruminants en France. Le premier pourrait impliquer le cerf comme espèce réservoir et les ruminants domestiques (entre autres) comme espèces sensibles, alors que le second impliquerait le chevreuil comme réservoir, sans impact significatif chez les bovins. Dans un deuxième temps, après avoir développé une technique de séquence capture pour A. phagocytophilum, nous avons séquencé et caractérisé le premier génome de cette bactérie issu d'un bovin. La comparaison de ce génome aux neuf autres génomes actuellement disponibles a permis d'identifier quatre protéines uniquement présentes chez la souche bovine, et neuf uniquement chez les deux souches de ruminants domestiques étudiés, ce qui amène à envisager leur implication potentielle dans le tropisme d'hôte de ces souches / Anaplasma phagocytophilum is an obligate intracellular alpha-proteobacterium mainly transmitted by Ixodes ticks. In domestic ruminants, it is the causative agent of tick-borne fever, which causes significant economic losses in Europe. It also infects a large range of hosts, including wild ruminants and rodents. The epidemiology of A. phagocytophilum is not yet fully understood. For example, the reservoir host(s) for European domestic ruminant strains has/have not been identified to date, which doesn't facilitate control of cattle infection. Our objective was to explore the genetic diversity of A. phagocytophilum obtained from ruminants in France. For this purpose, we first studied the circulation of this pathogen in domestic and wild ruminants, using a new MLVA technique. Our results potentially reveal the existence of at least two different epidemiological transmission cycles of A. phagocytophilum. The first cycle may involve red deer as reservoir hosts, and possibly domestic ruminants, as either accidental or longer-term hosts, whereas the second might involve roe deer. In a second study, we have sequenced and characterized the genome of A. phagocytophilum obtained from a cow. Following comparison with nine available genomes, we identified four genes specific to the A. phagocytophilum bovine genome, and nine common to both genomes from domestic ruminants (i.e. a cow and a sheep). These genes could be involved in host tropism of ruminant strains

La tuberculose est une maladie ancienne et ré-émergente qui constitue un véritable problème de santé publique dans le monde. L’émergence de la tuberculose à souches de M. tuberculosis multirésistantes et ultrarésistantes aux antituberculeux en plus de la pandémie du VIH/Sida, représentent un défi majeur dans la lutte contre la tuberculose pour son contrôle et son élimination. Ce contrôle de la tuberculose nécessite des mesures en santé publique et au niveau de l’individu. Ces mesures concernent la disponibilité et l’accessibilité à des tests de diagnostic rapides, des traitements efficaces et des outils de surveillance et de contrôle.Nos travaux concernent la recherche, le développement et la validation de méthodes moléculaires multiplexées, souvent basées sur le polymorphisme des loci CRISPR (Clustered Regularly Interspersed Palindromic Repeats). Elles sont rapides, à haut débit, moins onéreuses et applicables pour la santé publique (transmission de la tuberculose sensible et multirésistante, évaluation des programmes nationaux de tuberculose) mais aussi pour un meilleur diagnostic dans l’intérêt du patient (antibiogramme moléculaire, identification infra-spécifique). C’est ainsi que nous avons développé et validé le spoligoriftyping (méthode de génotypage combiné à la détection moléculaire de la résistance de M. tuberculosis à la rifampicine), le “TB-SPRINT” (Spoligoriftyping plus la détection moléculaire de la résistance à l’isoniazide) et le sous-typage de M. africanum. Ces différentes méthodes, aux performances (sensibilité/spécificité) satisfaisantes (99/100% pour le spoligoriftyping, 95/100% en moyenne pour le “TB-SPRINT”) ont servi à des études d’épidémiologie moléculaire dans des pays comme le Pakistan, le Nigéria et le Brésil. D’autres travaux en cours portent sur le génotypage basé sur les CRISPR d’autres espèces (Salmonella enterica, Legionella pneumophila) et sur des études de génomique comparative. Nos tests, utilisés en routine, replacent le laboratoire au cœur de la lutte anti-tuberculeuse et permettront d’importantes avancées en Santé Publique et Microbiologie médicale et environnementale. / Tuberculosis (TB) remains a major public health concern worldwide despite all the efforts to fight this disease. The emergence of multi drug and extensively drug resistant TB and the pandemic of HIV/AIDS constitute major threats and challenge for the TB control and eradication. TB control requires measures in public health and in individual level as accessibility to tests for early diagnostic, effective treatment and tools for tuberculosis surveillance and control.The goals of this work were research, development and validation of new molecular multiplexed methods based on polymorphism of the CRISPR (Clustered Regularly Interspersed Palindromic Repeats) loci and single nucleotides polymorphisms. These methods are rapid, high throughput, cheap and can be applied both for public health purposes (transmission of susceptible and multi-drug resistant tuberculosis, evaluation of national TB programs) as for interest of TB patient (drug resistance testing, infra-specific identification). Thus we developed spoligoriftyping and “TB-SPRINT” tests that allow genotyping and rifampicin or rifampicin and isoniazide resistance detection. Another test was developed for subtyping of M. africanum. All these methods had high performances (sensitivity/specificity), 99/100% for the spoligoriftyping and about 95/100% for the “TB-SPRINT” and were applied for molecular epidemiology studies of countries as Nigeria, Brazil and Pakistan. Other ongoing work and developments of genotyping methods are the spoligotyping of L. pneumophila and S. enterica and comparative genomics projects.Used in routine, our methods may play key roles in TB control and would allow important advances in Public Health, in medical and environmental Microbiology.

Introdução: Patógenos emergentes são isolados nas vias respiratórias de pacientes com fibrose cística (FC), entre eles a Burkholderia cepacia. Atualmente, é conhecida como um conjunto de nove espécies relacionadas (\"genomovares\"), referidas coletivamente como complexo B. cepacia. A identificação fenotípica do complexo B. cepacia é difícil, e métodos de análise do genoma bacteriano, como a reação em cadeia da polimerase, que exploram diferenças no gene recA, têm mostrado grande eficácia na caracterização dos genomovares. Alguns Centros de tratamento de FC demonstraram infecções cruzadas entre os pacientes e marcadores de virulência foram identificados com freqüência em alguns deles. Métodos baseados em biologia molecular são capazes de realizar a genotipagem das cepas e têm sido utilizados na avaliação epidemiológica. Objetivos: Identificar o genomovar e a presença de marcadores de virulência entre as cepas do complexo Burkholderia cepacia isoladas de pacientes com fibrose cística atendidos no ICr e analisar as cepas do complexo Burkholderia cepacia através de genotipagem pela técnica de RAPD. Métodos: Foram coletadas 672 amostras de escarro e esfregaço de orofaringe de 140 pacientes com fibrose cística (6 meses a 19 anos) atendidos na nossa Unidade nos períodos de set/2000 a abr/2001 e jun/2003 a jun/2004. As amostras foram cultivadas em meios seletivos, incluindo meio para B. cepacia, e a identificação realizada por sistema automatizado (1º período) e por testes fenotípicos clássicos (2º período). Após a extração do DNA, as cepas foram submetidas a uma série de reações de PCR para a determinação dos genomovares (I a VII), utilizando primers direcionados à amplificação de diferentes trechos da seqüência do gene recA, sendo, em seguida, submetidas ao seqüenciamento do DNA deste gene. Os genes de virulência pesquisados foram o cblA (que codifica o pili) e o esmR (marcador de uma cepa epidêmica). A genotipagem foi realizada pela técnica do RAPD, que analisa todo o genoma bacteriano. Resultados: Foram isoladas 41 cepas do complexo B. cepacia, obtidas de 21 pacientes com fibrose cística. O método de PCR identificou o genomovar de 32/41 (78%) das cepas e todos os resultados foram confirmados através do seqüenciamento do DNA. B. cenocepacia foi o genomovar mais prevalente (n = 17), seguido da B. multivorans (n = 12), B. vietnamiensis (n = 2) e B. cepacia (n = 1). As nove cepas não caracterizadas foram submetidas ao seqüenciamento, tendo sido encontradas 5 cepas de B. gladioli, 2 cepas de X. campestris e 2 cepas permaneceram sem identificação. O gene cblA não foi identificado em nenhuma cepa, mas o gene esmR foi encontrado em 2 amostras (pacientes não relacionados). A genotipagem detectou 23 padrões distintos, sem identificar padrões idênticos entre pacientes diferentes. Conclusões: O método de PCR baseado na amplificação do gene recA mostrou ser eficaz para a determinação do genomovar. B. cenocepacia e B. multivorans foram as espécies mais prevalentes entre nossos pacientes. A prevalência de marcadores de virulência foi baixa entre as cepas isoladas. Infecção cruzada pelo complexo B. cepacia não parece ter ocorrido na nossa Unidade durante os períodos estudados. / Introduction: Emerging pathogens are found in the respiratory tract of the cystic fibrosis (CF) patients, including the bacterium Burkholderia cepacia. At the present moment, it is recognized as a group of nine related species (\"genomovars\"), collectively referred as B. cepacia complex. Phenotypical identification of B. cepacia complex is difficult, and molecular based methods such as PCR, exploring differences in recA gene sequence, showed high efficacy for genomovar determination. B. cepacia complex cross infections among CF patients were previously described in some CF treatment Centers, and virulence markers were identified in a high frequency in some of them. Molecular based methods are suitable for strain genotyping and have been used for epidemiological evaluation. Aims: To identify genomovar status and virulence markers among Burkholderia cepacia complex isolates obtained from cystic fibrosis patients attending in the ICr, and to analyze the isolates through genotyping by RAPD. Methods: 672 sputum or oropharyngeal samples were obtained from 140 cystic fibrosis patients (6 months to 19 years) attending our Unit from sep/2000 to apr/2001 and jun/2003 to jun/2004. The samples were cultivated in selective media, including B. cepacia medium, and bacterial identification obtained by automated system (first period) and by classical phenotypic tests (second period). After DNA extraction, B. cepacia complex strains were submitted to sequential PCR reactions targeting recA gene in order to determine genomovar status (I to VII), and after that, submitted to automated DNA sequencing of this gene. Virulence genes screened were cblA (cable pilus) and esmR (epidemic strain marker). Genotyping was performed by whole bacterial genome fingerprinting using RAPD. Results: 41 isolates of B. cepacia complex were obtained from 21 cystic fibrosis patients. The PCR method identified genomovar status of 32/41 (78%) isolates and all results were confirmed by DNA sequencing. B. cenocepacia was the main genomovar (n=17), followed by B. multivorans (n = 12), B. vietnamiensis (n = 2) and B. cepacia (n = 1). The nine isolates uncharacterized were submitted to sequencing and we found 5 isolates as B. gladioli, 2 isolates as X. campestris and 2 isolates remained unidentified. The cblA gene was not identified in all isolates, but esmR gene was found on 2 strains (unrelated patients). Genotyping depicted 23 patterns, without identical patterns among different patients. Conclusions: The PCR method targeting recA gene showed to be a valuable tool for determination of genomovar status. B. cenocepacia and B. multivorans were the most prevalent specie among our patients. The prevalence of virulence markers was low among the isolates. Cross infection by B. cepacia complex does not seem to have occurred in our Unit during the two studied periods.

A elevada variabilidade genética do HIV tipo 1 e a seleção de mutações de resistência às drogas antirretrovirais tem representado um enorme desafio para o sucesso dos esquemas terapêuticos. Muitos estudos têm demonstrado que há padrões específicos de mutações para cada um dos subtipos de HIV-1. Os padrões do subtipo B são os mais bem definidos em função de sua presença majoritária nas epidemias da Europa e Estados Unidos. Contudo, a prevalência dos subtipos não-B, assim como a das formas recombinantes, tem aumentado significativamente em várias regiões. No Brasil, onde os subtipos B e F, e em alguns estados, também o C, coexistem, a presença de recombinantes BF vem ganhando destaque. Os objetivos deste trabalho foram comparar a região da protease do recombinante BF e do subtipo F puro quanto à possível presença de substituições diferentes, analisar o perfil mutacional e a covariação de mutações associadas ao tratamento e ao uso de inibidores específicos na protease do HIV-1 subtipo F e avaliar a reversão de mutações que já haviam sido selecionadas e a seleção de novas mutações após a troca do esquema terapêutico / The high genetic variability of HIV type 1 and the selection of antiretroviral resistance mutations have represented an enormous challenge to therapeutic schema success. Many studies have demonstrated that there are specific mutations patterns for each of the HIV-1 subtypes. Subtype B mutation profiles are the best studied due to its high presence in Europe and USA epidemics. However, prevalence of non-B subtypes, as well as recombinant forms, has been significantly increasing in many regions. In Brazil, where subtypes B and F, and in some states also C, have been co-circulating, BF recombinants are commonly found. The aims of this work were to compare protease region of BF recombinants to pure subtype F to search for different amino acid substitutions; analyzing mutation profile and co-variation of related-to-treatment mutations; verifying the relationship between the presence of groups of mutations and the use of specific antiretroviral drugs; and evaluating the selection of new mutations after changing therapeutic schema

O estudo foi desenvolvido com o intuito de detectar e caracterizar Cryptosporidium spp. em pacientes de diferentes comunidades brasileiras, atendidos no HC-FMUSP. A amostra utilizada foi de 2.410 amostras fecais, provenientes de exames realizados na Divisão de Laboratório Central do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (DLC-HCFMUSP), no período de 2000 a 2006. A maioria das amostras (96,82%) era oriunda do Estado de São Paulo (DIR 1 a DIR 24), sendo que 56,18% eram do Município de São Paulo (DIR 1). Foi avaliada, também, sua relação com outros enteroparasitos, com dados clínicos e localização geográfica. Todas as amostras fecais foram submetidas a métodos de concentração para pesquisa de enteroparasitos, com resultado positivo de 4,6% e 27,8% para helmintos e protozoários, respectivamente. Oocistos de Cryptosporidium spp. foram detectados, por microscopia óptica após coloração pelo método de Kinyoun em 233 amostras fecais (9,7%), semi quantificados e medidos. A maioria das amostras apresentava pequena quantidade de oocistos. Nos isolados biológicos obtidos foi feito a extração do DNA genômico utilizando 223 amostras fecais preservadas a 20°C negativos, incubadas com solução de lise (Tris-HCl + EDTA + SDS 10% + beta mercaptoetanol + PVP) e proteinase K seguida de extração com fenol-clorofórmio-álcool isoamílico (25:24:1) em tubo Phase Lock Gel light . A amplificação do DNA alvo foi feita com PCR dupla, tendo como marcador genético o gene 18 SSUrRNA. Os produtos da amplificação (amplicons) da PCR - Dupla foram digeridos pelas enzimas de restrição: TaqI e AseI. A PCR dupla confirmou Cryptosporidium em 37,2% (83/223) das amostras fecais analisadas, com sua caracterização em 62,7% (52/83) após a digestão de seus produtos. Foram observados perfis característicos de C. hominis (88,5%), C. parvum (3,8%), Cryptosporidium não parvum não hominis (34,9%) e infecções mistas com C. hominis (27,2%). Os não caracterizados foram considerados Cryptosporidium spp. Cryptosporidium spp. apresentou associações significativas com todos os grupos de riscos avaliados e diarréia. Foi observada correlação estatisticamente significativa entre tamanho dos oocistos detectados na microscopia e os genótipos Cryptosporidium hominis e Cryptosporidium não hominis não parvum. Conclui-se que diferentes genótipos de Cryptosporidium circulam em uma mesma região geográfica, infectando indivíduos tanto imunocompetentes como imunodeprimidos. A maior freqüência de Cryptosporidium hominis indica a rota fecal oral como a mais importante na transmissão desta infecção. Métodos moleculares de genotipagem são essenciais para estudos epidemiológicos deste organismo. / The study was developed with the purpose to detect and characterize Cryptosporidium spp. in patients of different Brazilian communities attended at the HC-FMSUP. Fecal samples from 2,410 individuals were arise from the Central Laboratory Division of the University of São Paulo Medical School Hospital (DLC-HC-FMUSP) searching for enteroparasites, in the period from 2000 to 2006. Most samples (96.82%) were from São Paulo state (DIR 1 to DIR 4) of which 58.18% were from São Paulo city (DIR 1). Their relationship with other enteroparasites, clinical data and geographical localization was also assessed. In the search for enteroparasites, all fecal samples were submitted to concentration methods with a 4.6% and 27.8% positive result for helminths and protozoans, respectively. Cryptosporidium spp. oocysts were detected, semi-quantified and measured in 233 fecal samples (9.7%), using light microscopy after staining by Kinyoun\'s method. Most samples presented few oocysts. In the biologic isolates genomic DNA extraction was performed using 223 fecal samples stored at -20oC, incubated with lysing solution (Tris-HCl + EDTA + 10% SDS + ? mercaptoethanol + PVP) and proteinase K followed by extraction with phenol-chloroform-isoamylic alcohol in a Phase Lock Gel Light tube. Amplification of target DNA was performed with double PCR, with 18 SSUrRNA gene as genetic marker. The double PCR amplification products (amplicons) were digested by TaqI and AseI restriction enzymes. Double PCR confirmed Cryptosporidium in 37.2% (83/223) of the analyzed fecal samples with characterization in 62.7% (52/83) after digestion of its products. Characteristic profiles of C. hominis (88.5%). C. parvum (3.8%), Cryptosporidium non-parvum non-hominis (34.9%) and mixed infection with C. hominis (27.2%) were observed. Those not characterized were considered to be Cryptosporidium spp. Cryptopsoridium hominis presented significant associations with all evaluated risk groups and diarrhea. A statistically significant correlation between size of the oocysts detected by microscopy and the Cryptosporidium hominis and Cryptosporidium non-hominis non-parvum genotypes was observed. It is concluded that different Cryptosporidium genotypes circulate in the same geographical region, infecting both immunocompetent and immunodepressed individuals. The higher frequency of Cryptosporidium hominis indicates the fecal-oral pathway as the most important in the transmission of this infection. Molecular genotyping methods are essential for epidemiological studies on this parasite.

Introdução: Patógenos emergentes são isolados nas vias respiratórias de pacientes com fibrose cística (FC), entre eles a Burkholderia cepacia. Atualmente, é conhecida como um conjunto de nove espécies relacionadas (\"genomovares\"), referidas coletivamente como complexo B. cepacia. A identificação fenotípica do complexo B. cepacia é difícil, e métodos de análise do genoma bacteriano, como a reação em cadeia da polimerase, que exploram diferenças no gene recA, têm mostrado grande eficácia na caracterização dos genomovares. Alguns Centros de tratamento de FC demonstraram infecções cruzadas entre os pacientes e marcadores de virulência foram identificados com freqüência em alguns deles. Métodos baseados em biologia molecular são capazes de realizar a genotipagem das cepas e têm sido utilizados na avaliação epidemiológica. Objetivos: Identificar o genomovar e a presença de marcadores de virulência entre as cepas do complexo Burkholderia cepacia isoladas de pacientes com fibrose cística atendidos no ICr e analisar as cepas do complexo Burkholderia cepacia através de genotipagem pela técnica de RAPD. Métodos: Foram coletadas 672 amostras de escarro e esfregaço de orofaringe de 140 pacientes com fibrose cística (6 meses a 19 anos) atendidos na nossa Unidade nos períodos de set/2000 a abr/2001 e jun/2003 a jun/2004. As amostras foram cultivadas em meios seletivos, incluindo meio para B. cepacia, e a identificação realizada por sistema automatizado (1º período) e por testes fenotípicos clássicos (2º período). Após a extração do DNA, as cepas foram submetidas a uma série de reações de PCR para a determinação dos genomovares (I a VII), utilizando primers direcionados à amplificação de diferentes trechos da seqüência do gene recA, sendo, em seguida, submetidas ao seqüenciamento do DNA deste gene. Os genes de virulência pesquisados foram o cblA (que codifica o pili) e o esmR (marcador de uma cepa epidêmica). A genotipagem foi realizada pela técnica do RAPD, que analisa todo o genoma bacteriano. Resultados: Foram isoladas 41 cepas do complexo B. cepacia, obtidas de 21 pacientes com fibrose cística. O método de PCR identificou o genomovar de 32/41 (78%) das cepas e todos os resultados foram confirmados através do seqüenciamento do DNA. B. cenocepacia foi o genomovar mais prevalente (n = 17), seguido da B. multivorans (n = 12), B. vietnamiensis (n = 2) e B. cepacia (n = 1). As nove cepas não caracterizadas foram submetidas ao seqüenciamento, tendo sido encontradas 5 cepas de B. gladioli, 2 cepas de X. campestris e 2 cepas permaneceram sem identificação. O gene cblA não foi identificado em nenhuma cepa, mas o gene esmR foi encontrado em 2 amostras (pacientes não relacionados). A genotipagem detectou 23 padrões distintos, sem identificar padrões idênticos entre pacientes diferentes. Conclusões: O método de PCR baseado na amplificação do gene recA mostrou ser eficaz para a determinação do genomovar. B. cenocepacia e B. multivorans foram as espécies mais prevalentes entre nossos pacientes. A prevalência de marcadores de virulência foi baixa entre as cepas isoladas. Infecção cruzada pelo complexo B. cepacia não parece ter ocorrido na nossa Unidade durante os períodos estudados. / Introduction: Emerging pathogens are found in the respiratory tract of the cystic fibrosis (CF) patients, including the bacterium Burkholderia cepacia. At the present moment, it is recognized as a group of nine related species (\"genomovars\"), collectively referred as B. cepacia complex. Phenotypical identification of B. cepacia complex is difficult, and molecular based methods such as PCR, exploring differences in recA gene sequence, showed high efficacy for genomovar determination. B. cepacia complex cross infections among CF patients were previously described in some CF treatment Centers, and virulence markers were identified in a high frequency in some of them. Molecular based methods are suitable for strain genotyping and have been used for epidemiological evaluation. Aims: To identify genomovar status and virulence markers among Burkholderia cepacia complex isolates obtained from cystic fibrosis patients attending in the ICr, and to analyze the isolates through genotyping by RAPD. Methods: 672 sputum or oropharyngeal samples were obtained from 140 cystic fibrosis patients (6 months to 19 years) attending our Unit from sep/2000 to apr/2001 and jun/2003 to jun/2004. The samples were cultivated in selective media, including B. cepacia medium, and bacterial identification obtained by automated system (first period) and by classical phenotypic tests (second period). After DNA extraction, B. cepacia complex strains were submitted to sequential PCR reactions targeting recA gene in order to determine genomovar status (I to VII), and after that, submitted to automated DNA sequencing of this gene. Virulence genes screened were cblA (cable pilus) and esmR (epidemic strain marker). Genotyping was performed by whole bacterial genome fingerprinting using RAPD. Results: 41 isolates of B. cepacia complex were obtained from 21 cystic fibrosis patients. The PCR method identified genomovar status of 32/41 (78%) isolates and all results were confirmed by DNA sequencing. B. cenocepacia was the main genomovar (n=17), followed by B. multivorans (n = 12), B. vietnamiensis (n = 2) and B. cepacia (n = 1). The nine isolates uncharacterized were submitted to sequencing and we found 5 isolates as B. gladioli, 2 isolates as X. campestris and 2 isolates remained unidentified. The cblA gene was not identified in all isolates, but esmR gene was found on 2 strains (unrelated patients). Genotyping depicted 23 patterns, without identical patterns among different patients. Conclusions: The PCR method targeting recA gene showed to be a valuable tool for determination of genomovar status. B. cenocepacia and B. multivorans were the most prevalent specie among our patients. The prevalence of virulence markers was low among the isolates. Cross infection by B. cepacia complex does not seem to have occurred in our Unit during the two studied periods.

A Febre Maculosa Brasileira causada por riquétsias do Grupo Febre Maculosa (GFM) e transmitida por carrapatos ocorre principalmente na Região Sudeste, onde óbitos humanos são registrados. No estado do Rio de Janeiro, a letalidade devido à riquetsiose é alta, mas só recentemente investigações epidemiológicas foram realizadas, e indicaram a participação de novas espécies de ectoparasitas na circulação das riquétsias. O objetivo geral do projeto é avaliar riquétsias em ectoparasitos coletados em áreas de casos humanos de Febre Maculosa, suspeitos, compatíveis ou confirmados, em municípios do estado com focos recentemente comunicados. A detecção e análise de genes riquetsiais indicam a presença de Rickettsia bellii, Rickettsia felis e Rickettsia rickettsii, nos vetores Amblyomma cajennense, Amblyomma dubitatum, Boophilus microplus, Ctenocephalides felis e Ctenocephalides canis, sugerindo ampla distribuição geográfica de riquétsias GFM, nas regiões Serrana, Noroeste Fluminense e Médio Paraíba do estado. / Brazilian spotted fever caused by spotted fever group (SFG) rickettsiae and mainly transmitted by ticks occurs in the southeast, where human deaths are recorded. In the state of Rio de Janeiro, lethality due to rickettsial infection is high, but only recently epidemiological investigations were conducted, and indicated the participation of new species of ectoparasites in rickettsiae circulation. The project\'s overall objective is to evaluate rickettsiae in ectoparasites collected in areas of human suspected, confirmed or compatible cases of spotted fever, in cities of the State with the recently reported outbreaks. The detection and analysis of rickettsial genes indicate the presence of Rickettsia bellii, Rickettsia felis and Rickettsia rickettsii in the vectors Amblyomma cajennense, Amblyomma dubitatum, Boophilus microplus, Ctenocephalides felis and Ctenocephalides canis, suggesting broad geographic distribution of SFG rickettsiae in the regions Serrana, Noroeste Fluminense and Médio Paraíba of the State.

Thesis (MSc (Biomedical Technology))--Cape Peninsula University of Technology, 2017. / Background: It is well established that Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogenic organism that has been frequently identified as the cause of nosocomial and community acquired infections. Furthermore, studies have shown that over the last few decades strains of the genus Klebsiella have systematically developed resistance to numerous antibiotics. Aims and Methods: The primary aim of this study was to investigate the prevalence of K. pneumoniae in nosocomial and community isolates in the Western Cape province of South Africa. Various identification techniques such as the polymerase chain reaction (PCR) using the API 20 E, the VITEK®2 system, primers specific for the 16S-23S rDNA ITS region and the Matrix-assisted laser desorption/ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) were compared for the identification of this pathogen. The VITEK 2 system was used to detect antibiotic resistant profiles of the K. pneumoniae isolates and to identify the extended spectrum beta-lactamase (ESBL) phenotypic among these isolates. The PCR was used to detect Beta-lactam genes viz. CTX-M (blaCTX-M), TEM (blaTEM) and SHV (blaSHV) respectively in both the genome and plasmid DNA of K. pneumoniae using gene specific primers. Results: In total 57 agar plate bacterial cultures or glycerol stock bacterial cultures were obtained during 2011. Of the 57 isolates, the API 20 E test identified 47 (82.5%) of the isolates (n = 57) as K. pneumoniae while 10 isolates (17.5%) were identified as Raoultella species. The VITEK 2 method and PCR identified all 57 isolates as K. pneumoniae (100%). Of the isolates, 82.5% (47/57) were positively identified as Klebsiella species, 14% (8/57) were identified as Klebsiella variicola and 3.5% (2/57) were shown as no reliable identification (NRI) when using the MALDI-TOF MS. Examination of the 57 isolates using primers specific for the CTX-M (blaCTX-M), TEM (blaTEM) and SHV (blaSHV) respectively showed the following: PCR amplicons for the TEM gene were produced successfully for 46 (81%) of the 57 isolates included in this project, while 11 (19%) of the samples did not yield any TEM amplicons; PCR amplicons for the blaSHV gene were obtained successfully for 56 (98%) of the 57 DNA samples, while 1 sample (2%) did not yield any SHV amplicons; and PCR amplicons for the blaCTX-M gene were produced successfully by 89% (n = 51) of the DNA samples included in this project, while 11% (n = 6) did not yield any CTX-M amplicon. Extended-spectrum beta-lactamase phenotypes had been confirmed in 84% (n = 48) K. pneumoniae isolates while nine isolates were found to be non-ESBL. Resistance rates for these 48 isolates were high and showed resistance patterns of: Amoxicillin/Ampicillin, Amoxycillin/Clavulanate, Ceftriaxone/Cefotaxime, Cefuroxime/Cefprozil and Ceftazidime (100%, n = 48); Piperacillin/Tazobactam and Cefoxitin (98%, 47/48); Cefepime (96%, 46/48); Aztreonam (94%; 45/48); Tobramycin (81%, 39/48); Gentamycin and Ciprofloxacin (77%, 37/48); Trimethoprim/Sulfamethoxazole (67%, 32/48); and Tigecycline (25% 12/48). Conclusion: For the analysis by all four methods employed, a total agreement of 68.4% was obtained, indicating the positive identification of K. pneumoniae in 39 of the 57 samples analysed. An average agreement of 28.1% was then obtained for the comparison of results generated for three of the methods utilised, while a 3.5% average agreement was obtained for at least two methods. Furthermore, all four methods agreed that 82.5% of the isolates were Klebsiella species while three methods agreed that 17.5% of the isolates were Klebsiella species. Based on the results obtained in the current study, PCR and VITEK 2 were the methods of choice for the identification of K. pneumoniae. The current study also showed, that ESBL-K. pneumoniae strains are present in the Western Cape province, South Africa; with high resistance profiles to numerous antibiotics including the Cephalosporins.

O estudo foi desenvolvido com o intuito de detectar e caracterizar Cryptosporidium spp. em pacientes de diferentes comunidades brasileiras, atendidos no HC-FMUSP. A amostra utilizada foi de 2.410 amostras fecais, provenientes de exames realizados na Divisão de Laboratório Central do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (DLC-HCFMUSP), no período de 2000 a 2006. A maioria das amostras (96,82%) era oriunda do Estado de São Paulo (DIR 1 a DIR 24), sendo que 56,18% eram do Município de São Paulo (DIR 1). Foi avaliada, também, sua relação com outros enteroparasitos, com dados clínicos e localização geográfica. Todas as amostras fecais foram submetidas a métodos de concentração para pesquisa de enteroparasitos, com resultado positivo de 4,6% e 27,8% para helmintos e protozoários, respectivamente. Oocistos de Cryptosporidium spp. foram detectados, por microscopia óptica após coloração pelo método de Kinyoun em 233 amostras fecais (9,7%), semi quantificados e medidos. A maioria das amostras apresentava pequena quantidade de oocistos. Nos isolados biológicos obtidos foi feito a extração do DNA genômico utilizando 223 amostras fecais preservadas a 20°C negativos, incubadas com solução de lise (Tris-HCl + EDTA + SDS 10% + beta mercaptoetanol + PVP) e proteinase K seguida de extração com fenol-clorofórmio-álcool isoamílico (25:24:1) em tubo Phase Lock Gel light . A amplificação do DNA alvo foi feita com PCR dupla, tendo como marcador genético o gene 18 SSUrRNA. Os produtos da amplificação (amplicons) da PCR - Dupla foram digeridos pelas enzimas de restrição: TaqI e AseI. A PCR dupla confirmou Cryptosporidium em 37,2% (83/223) das amostras fecais analisadas, com sua caracterização em 62,7% (52/83) após a digestão de seus produtos. Foram observados perfis característicos de C. hominis (88,5%), C. parvum (3,8%), Cryptosporidium não parvum não hominis (34,9%) e infecções mistas com C. hominis (27,2%). Os não caracterizados foram considerados Cryptosporidium spp. Cryptosporidium spp. apresentou associações significativas com todos os grupos de riscos avaliados e diarréia. Foi observada correlação estatisticamente significativa entre tamanho dos oocistos detectados na microscopia e os genótipos Cryptosporidium hominis e Cryptosporidium não hominis não parvum. Conclui-se que diferentes genótipos de Cryptosporidium circulam em uma mesma região geográfica, infectando indivíduos tanto imunocompetentes como imunodeprimidos. A maior freqüência de Cryptosporidium hominis indica a rota fecal oral como a mais importante na transmissão desta infecção. Métodos moleculares de genotipagem são essenciais para estudos epidemiológicos deste organismo. / The study was developed with the purpose to detect and characterize Cryptosporidium spp. in patients of different Brazilian communities attended at the HC-FMSUP. Fecal samples from 2,410 individuals were arise from the Central Laboratory Division of the University of São Paulo Medical School Hospital (DLC-HC-FMUSP) searching for enteroparasites, in the period from 2000 to 2006. Most samples (96.82%) were from São Paulo state (DIR 1 to DIR 4) of which 58.18% were from São Paulo city (DIR 1). Their relationship with other enteroparasites, clinical data and geographical localization was also assessed. In the search for enteroparasites, all fecal samples were submitted to concentration methods with a 4.6% and 27.8% positive result for helminths and protozoans, respectively. Cryptosporidium spp. oocysts were detected, semi-quantified and measured in 233 fecal samples (9.7%), using light microscopy after staining by Kinyoun\'s method. Most samples presented few oocysts. In the biologic isolates genomic DNA extraction was performed using 223 fecal samples stored at -20oC, incubated with lysing solution (Tris-HCl + EDTA + 10% SDS + ? mercaptoethanol + PVP) and proteinase K followed by extraction with phenol-chloroform-isoamylic alcohol in a Phase Lock Gel Light tube. Amplification of target DNA was performed with double PCR, with 18 SSUrRNA gene as genetic marker. The double PCR amplification products (amplicons) were digested by TaqI and AseI restriction enzymes. Double PCR confirmed Cryptosporidium in 37.2% (83/223) of the analyzed fecal samples with characterization in 62.7% (52/83) after digestion of its products. Characteristic profiles of C. hominis (88.5%). C. parvum (3.8%), Cryptosporidium non-parvum non-hominis (34.9%) and mixed infection with C. hominis (27.2%) were observed. Those not characterized were considered to be Cryptosporidium spp. Cryptopsoridium hominis presented significant associations with all evaluated risk groups and diarrhea. A statistically significant correlation between size of the oocysts detected by microscopy and the Cryptosporidium hominis and Cryptosporidium non-hominis non-parvum genotypes was observed. It is concluded that different Cryptosporidium genotypes circulate in the same geographical region, infecting both immunocompetent and immunodepressed individuals. The higher frequency of Cryptosporidium hominis indicates the fecal-oral pathway as the most important in the transmission of this infection. Molecular genotyping methods are essential for epidemiological studies on this parasite.

A elevada variabilidade genética do HIV tipo 1 e a seleção de mutações de resistência às drogas antirretrovirais tem representado um enorme desafio para o sucesso dos esquemas terapêuticos. Muitos estudos têm demonstrado que há padrões específicos de mutações para cada um dos subtipos de HIV-1. Os padrões do subtipo B são os mais bem definidos em função de sua presença majoritária nas epidemias da Europa e Estados Unidos. Contudo, a prevalência dos subtipos não-B, assim como a das formas recombinantes, tem aumentado significativamente em várias regiões. No Brasil, onde os subtipos B e F, e em alguns estados, também o C, coexistem, a presença de recombinantes BF vem ganhando destaque. Os objetivos deste trabalho foram comparar a região da protease do recombinante BF e do subtipo F puro quanto à possível presença de substituições diferentes, analisar o perfil mutacional e a covariação de mutações associadas ao tratamento e ao uso de inibidores específicos na protease do HIV-1 subtipo F e avaliar a reversão de mutações que já haviam sido selecionadas e a seleção de novas mutações após a troca do esquema terapêutico / The high genetic variability of HIV type 1 and the selection of antiretroviral resistance mutations have represented an enormous challenge to therapeutic schema success. Many studies have demonstrated that there are specific mutations patterns for each of the HIV-1 subtypes. Subtype B mutation profiles are the best studied due to its high presence in Europe and USA epidemics. However, prevalence of non-B subtypes, as well as recombinant forms, has been significantly increasing in many regions. In Brazil, where subtypes B and F, and in some states also C, have been co-circulating, BF recombinants are commonly found. The aims of this work were to compare protease region of BF recombinants to pure subtype F to search for different amino acid substitutions; analyzing mutation profile and co-variation of related-to-treatment mutations; verifying the relationship between the presence of groups of mutations and the use of specific antiretroviral drugs; and evaluating the selection of new mutations after changing therapeutic schema